
The following are the corresponding clients for the QIAGEN CLC Genomics Server 21.0.6.
We recommend running the corresponding versions of clients for QIAGEN CLC Genomics Server. However, QIAGEN CLC Genomics Workbench 21.0.1, 21.0.2, 21.0.3. 21.0.4 and 21.0.5, QIAGEN CLC Main Workbench 21.0.1, 21.0.2, 21.0.3, 21.0.4 and 21.0.5, and QIAGEN CLC Command Line Tools 21.0.1, 21.0.2, 21.0.3, 21.0.4 and 21.0.5 can also connect to QIAGEN CLC Genomics Server 21.0.6.
CLC Command Line Tools 21.0.6 is the corresponding client for QIAGEN CLC Genomics Server 21.0.6.
CLC Command Line Tools 21.0.6 is the corresponding client for QIAGEN CLC Genomics Server 21.0.6.
CLC Command Line Tools 21.0.6 can also act as a client for the QIAGEN CLC Genomics Server 21.0.1, 21.0.2, 21.0.3, 21.0.4 and 21.0.5. However, we recommend running the corresponding version.
The following are the corresponding clients for the QIAGEN CLC Genomics Server 21.0.5.
We recommend running the corresponding versions of clients for QIAGEN CLC Genomics Server. However, QIAGEN CLC Genomics Workbench 21.0.1, 21.0.2, 21.0.3 and 21.0.4, QIAGEN CLC Main Workbench 21.0.1, 21.0.2, 21.0.3 and 21.0.4, and QIAGEN CLC Command Line Tools 21.0.1, 21.0.2, 21.0.3 and 21.0.4 can also connect to QIAGEN CLC Genomics Server 21.0.5.
We will not be distributing the Genomics Analysis Portal functionality from the CLC Genomics Server distribution with the next major release.
The following will be removed in a future release of the software:
CLC Command Line Tools 21.0.5 is the corresponding client for QIAGEN CLC Genomics Server 21.0.5.
CLC Command Line Tools 21.0.5 can also act as a client for the QIAGEN CLC Genomics Server 21.0.1, 21.0.2, 21.0.3 and 21.0.4. However, we recommend running the corresponding version.
Changes have been made that improve the speed of jobs on the CLC Genomics Cloud Engine (GCE) that involve large CLC data elements. This improvement affects systems where the Cloud Server Plugin is installed and GCE-related Cloud Plugin settings have been settings have been configured.
The location of reference data available for download from QIAGEN via the CLC Genomics Server (e.g. QIAGEN reference sets, protein and resistance databases) is changing. The list of sites for configuring firewall settings for networks that utilize a whitelist approach are:
No configuration changes are needed in the CLC Server Workbench itself. The full list of sites the software accesses is available in our FAQ entry: Which internet addresses does CLC software need access to?
We are considering retiring the recently introduced Genomics Analyis Portal functionality. If this would affect your work, please get in touch with us about this by emailing us at ts-bioinformatics@qiagen.com.
The following are the corresponding clients for the QIAGEN CLC Genomics Server 21.0.4.
We recommend running the corresponding versions of clients for QIAGEN CLC Genomics Server. However, QIAGEN CLC Genomics Workbench 21.0.1, 21.0.2 and 21.0.3, QIAGEN CLC Main Workbench 21.0.1, 21.0.2 and 21.0.3, and QIAGEN CLC Command Line Tools 21.0.1, 21.0.2 and 21.0.3 can also connect to QIAGEN CLC Genomics Server 21.0.4.
CLC Command Line Tools 21.0.4 is the corresponding client for QIAGEN CLC Genomics Server 21.0.4.
CLC Command Line Tools 21.0.4 is the corresponding client for QIAGEN CLC Genomics Server 21.0.4.
CLC Command Line Tools 21.0.4 can also act as a client for the QIAGEN CLC Genomics Server 21.0.1, 21.0.2 and 21.0.3. However, we recommend running the corresponding version.
The following are the corresponding clients for the QIAGEN CLC Genomics Server 21.0.3.
We recommend running the corresponding versions of clients for QIAGEN CLC Genomics Server. However, QIAGEN CLC Genomics Workbench 21.0.1 and 21.0.2, QIAGEN CLC Main Workbench 21.0.1 and 21.0.2, and QIAGEN CLC Command Line Tools 21.0.1 and 21.0.2 can also connect to QIAGEN CLC Genomics Server 21.0.3.
CLC Command Line Tools 21.0.3 is the corresponding client for QIAGEN CLC Genomics Server 21.0.3.
CLC Command Line Tools 21.0.3 can also act as a client for the QIAGEN CLC Genomics Server 21.0.1 and 21.0.1. However, we recommend running the corresponding version.
The following are the corresponding clients for the QIAGEN CLC Genomics Server 21.0.2.
We recommend running the corresponding versions of clients for QIAGEN CLC Genomics Server. However, QIAGEN CLC Genomics Workbench 21.0.1, QIAGEN CLC Main Workbench 21.0.1, and QIAGEN CLC Command Line Tools 21.0.1 can also connect to QIAGEN CLC Genomics Server 21.0.1.
CLC Command Line Tools 21.0.2 is the corresponding client for QIAGEN CLC Genomics Server 21.0.2. It can also act as a client for the QIAGEN CLC Genomics Server 21.0.1. We recommend running the corresponding version of the CLC Command Line Tools CLC Genomics Server.
This is a compatibility release for the corresponding client software, QIAGEN CLC Genomics Workbench 21.0.1 and QIAGEN CLC Main Workbench 21.0.1.
Please see the release notes for CLC Genomics Server 21.0, below, for a full list of changes since the last general release of this software.
The following are the corresponding clients for the QIAGEN CLC Genomics Server 21.0.1.
We recommend running the corresponding versions of clients for QIAGEN CLC Genomics Server. However, QIAGEN CLC Genomics Workbench 21.0, QIAGEN CLC Main Workbench 21.0, and QIAGEN CLC Command Line Tools 21.0 can also connect to QIAGEN CLC Genomics Server 21.0.1.
This is a compatibility release, as the corresponding client for the QIAGEN CLC Genomics Server 21.0.1.
Please see the release notes for CLC Server Command Line Tools 21.0, below, for a full list of changes since the last general release of this software.
CLC Command Line Tools 21.0.1 is the corresponding client for QIAGEN CLC Genomics Server 21.0.1. It can also act as a client for the QIAGEN CLC Genomics Server 21.0. We recommend running the corresponding version of the CLC Command Line Tools CLC Genomics Server.
Software licenses and server plugins can be downloaded and updated directly via the web administrative interface, under the new Extensions tab. In association with this, plugin management has been moved to the new Extensions tab, and the display of information about installed plugins has been improved.
The Genomics Analysis Portal is a web browser based, graphical client for the the CLC Genomics Server. Workflows can be submitted for analysis on the server from a web browser, analysis progress and status of analyses can be monitored, and results can be downloaded.
Enabling the Genomics Analysis Portal is described in the CLC Server Admin manual, while configuration and use is described in the Genomics Analysis Portal manual.
Portable, “containerized” external applications using Docker are supported on Linux-based CLC Server setups. Containers can be local or in a repository, such as Amazon Elastic Container Repository (AWS ECR) or Docker Hub. Like standard external applications, they can be run as individual tools or included in workflows.
One or more File system locations can be configured to be used for “user home” folders, which are top-level folders within that location. A user is granted write access only to the folder with a name matching their username. These “user home” folders can be created automatically on user login, or created manually for select users.
New features have been introduced, and improvements made, to support automated analyses of Sanger trace data using workflows.
Extract IsomiR Counts, Annotate with Repeat and Homopolymer Information and Merge Variant Tracks were previously available via the Biomedical Genomics Analysis Server Plugin.
The follow are the corresponding client applications for CLC Genomics Server 21.0
CLC Genomics Server 21.0 is compatible with GCE version 21.0.
The following will be removed in a future release of the software:
The following are the corresponding clients for the QIAGEN CLC Genomics Server 20.0.5.
We recommend running the corresponding versions of clients for QIAGEN CLC Genomics Server. However, QIAGEN CLC Genomics Workbench 20.0, 20.0.1, 20.0.2, 20.0.3 and 20.0.4, QIAGEN CLC Main Workbench 20.0, 20.0.1, 20.0.2, 20.0.3 and 20.0.4, and QIAGEN CLC Command Line Tools 20.0, 20.0.1, 20.0.2, 20.0.3 and 20.0.4 can also connect to QIAGEN CLC Genomics Server 20.0.5. Tools that have changed between versions cannot be launched when using compatible, but not corresponding, client-server combinations.
Fixed an issue that caused information about libraries intended for the LICENSE and NOTICE files to be omitted.
CLC Command Line Tools 20.0.5 is the corresponding client for QIAGEN CLC Genomics Server 20.0.5.
CLC Command Line Tools 20.0.5 can also act as a client for the QIAGEN CLC Genomics Server 20.0, 20.0.1, 20.0.2, 20.0.3 and 20.0.4. However, we recommend running the corresponding version.
The following are the corresponding clients for the QIAGEN CLC Genomics Server 20.0.4.
We recommend running the corresponding versions of clients for QIAGEN CLC Genomics Server. However, QIAGEN CLC Genomics Workbench 20.0, 20.0.1, 20.0.2, and 20.0.3, QIAGEN CLC Main Workbench 20.0, 20.0.1, 20.0.2, and 20.0.3, and QIAGEN CLC Command Line Tools 20.0, 20.0.1, 20.0.2, and 20.0.3 can also connect to QIAGEN CLC Genomics Server 20.0.4. Tools that have changed between versions cannot be launched when using compatible, but not corresponding, client-server combinations.
The following tools will be removed in a future release of the software:
The following functionality will be removed in a future release:
If you are concerned about these proposed changes, please contact our Support team by emailing ts-bioinformatics@qiagen.com.
CLC Command Line Tools 20.0.4 is the corresponding client for QIAGEN CLC Genomics Server 20.0.4.
CLC Command Line Tools 20.0.4 can also act as a client for the QIAGEN CLC Genomics Server 20.0, 20.0.1, 20.0.2, and 20.0.3. However, we recommend running the corresponding version.
The following are the corresponding clients for the QIAGEN CLC Genomics Server 20.0.3.
We recommend running the corresponding versions of clients for QIAGEN CLC Genomics Server. However, QIAGEN CLC Genomics Workbench 20.0, 20.0.1 and 20.0.2, QIAGEN CLC Main Workbench 20.0, 20.0.1 and 20.0.2, and QIAGEN CLC Command Line Tools 20.0, 20.0.1 and 20.0.2 can also connect to QIAGEN CLC Genomics Server 20.0.3. Tools that have changed between versions cannot be launched when using compatible, but not corresponding, client-server combinations.
If you are concerned about these proposed changes, please contact our Support team by emailing ts-bioinformatics@qiagen.com.
CLC Command Line Tools 20.0.3 is the corresponding client for QIAGEN CLC Genomics Server 20.0.3.
CLC Command Line Tools 20.0.3 can also act as a client for the QIAGEN CLC Genomics Server 20.0, 20.0.1 and 20.0.3. However, we recommend running the corresponding version.
NCBI plans to change their blast database folder structure in early February 2020. When that happens, the Download BLAST Databases tool of CLC Genomics Server 20.0.2, and future updates, will list the new, dbV5 blast databases for download. The Create Blast Database tool will continue to create dbV4 databases. Databases of either version can be searched using the blast programs included in QIAGEN CLC Genomics Server 20.x release line.
The following are the corresponding clients for the QIAGEN CLC Genomics Server 20.0.2.
We recommend running the corresponding versions of clients for QIAGEN CLC Genomics Server. However, QIAGEN CLC Genomics Workbench 20.0 and 20.0.1, QIAGEN CLC Main Workbench 20.0 and 20.0.1, and QIAGEN CLC Command Line Tools 20.0 and 20.0.1 can also connect to QIAGEN CLC Genomics Server 20.0.2. Tools that have changed between versions cannot be launched when using compatible, but not corresponding, client-server combinations.
The following tools will be removed in a future release of the software:
The “Run in Batch Mode” functionality used for launching workflows with multiple inputs from a CLC Workbench is now legacy. Such workflows can now be launched in batch mode from a CLC Workbench by checking the “Batch” checkbox when selecting the input data.
If you are concerned about these proposed changes, please contact our Support team by emailing ts-bioinformatics@qiagen.com.
This is a compatibility release of the corresponding client for QIAGEN CLC Genomics Server 20.0.2.
CLC Command Line Tools 20.0.2 is the corresponding client for QIAGEN CLC Genomics Server 20.0.2.
CLC Command Line Tools 20.0.2 can also act as a client for the QIAGEN CLC Genomics Server 20.0 and CLC Genomics Server 20.0.2. However, we recommend running the corresponding version of the CLC Command Line Tools CLC Genomics Server.
We recommend running the corresponding versions of clients for CLC Genomics Server. However, CLC Genomics Workbench 20.0, CLC Main Workbench 20.0, and CLC Command Line Tools 20.0 can also connect to CLC Genomics Server 20.0. Tools that have changed between versions cannot be launched when using compatible, but not corresponding, client-server combinations.
The following tools will be removed in a future release of the software:
The “Run in Batch Mode” functionality used for launching workflows with multiple inputs from a CLC Workbench is now legacy. Such workflows can now be launched in batch mode from a CLC Workbench by checking the “Batch” checkbox when selecting the input data.
If you are concerned about these proposed changes, please contact our Support team by emailing ts-bioinformatics@qiagen.com.
CLC Command Line Tools 20.0.1 is the corresponding client for CLC Genomics Server 20.0.1.
CLC Command Line Tools 20.0.1 can also act as a client for the CLC Genomics Server 20.0. However, we recommend running the corresponding version of the CLC Command Line Tools CLC Genomics Server.
The administrative interface for External Applications has been reworked, providing better support for administration, configuration and collaborative development. Changes include:
The following tools have been retired:
The import of the following formats is no longer supported:
The follow are the corresponding client applications for QIAGEN CLC Genomics Server 20.0
Functionality of the following plugins has been integrated into the QIAGEN CLC Genomics Server:
The following tools will be removed in a future release of the software:
The “Run in Batch Mode” functionality used for launching workflows with multiple inputs from a CLC Workbench is now legacy. Such workflows can now be launched in batch mode from a CLC Workbench by checking the “Batch” checkbox when selecting the input data.
If you are concerned about these proposed changes, please contact our Support team by emailing ts-bioinformatics@qiagen.com.
Please see the QIAGEN CLC Genomics Server 20.0 listings above for the details about the new tools and features listed here.
Tools for detecting peaks in sequencing data are now available and can be called using the following commands:
The first three of these commands were formerly available via the Advanced Peak Shape Tools Server Plugin (beta), and the fourth via the Histone ChIP-Seq Server Plugin.
Tools for analyzing miRNA data are now available and can be called using the following commands:
These commands were formerly available via the Biomedical Genomics Analysis Server Plugin.
If you are concerned about these proposed changes, please contact our Support team by emailing ts-bioinformatics@qiagen.com.
Various minor improvements
The following are the corresponding clients for the QIAGEN CLC Genomics Server 11.0.4.
We recommend running the corresponding versions of clients for QIAGEN CLC Genomics Server. However, QIAGEN CLC Genomics Workbench 12.0, 12.0.1, 12.0.2 and 12.0.3, QIAGEN CLC Main Workbench 8.1, 8.1.1, 8.1.2 and 8.1.3, and QIAGEN CLC Command Line Tools 6.0, 6.0.1, 6.0.2 and 6.0.3 can also connect to QIAGEN CLC Genomics Server 11.0.4. Tools that have changed between versions cannot be launched when using compatible, but not corresponding, client-server combinations.
QIAGEN CLC Command Line Tools 6.0.4 is the corresponding client for QIAGEN CLC Genomics Server 11.0.4.
QIAGEN CLC Command Line Tools 6.0.4 can also act as a client for the QIAGEN CLC Genomics Server 11.0, 11.0.1, 11.0.2 and 11.0.3. However, we recommend running the corresponding versions of client and server software.
The following are the corresponding clients for the QIAGEN CLC Genomics Server 11.0.3.
We recommend running the corresponding versions of clients for QIAGEN CLC Genomics Server. However, QIAGEN CLC Genomics Workbench 12.0, 12.0.1, and 12.0.2, QIAGEN CLC Main Workbench 8.1, 8.1.1, and 8.1.2, and QIAGEN CLC Command Line Tools 6.0, 6.0.1, and 6.0.2 can also connect to QIAGEN CLC Genomics Server 11.0.3. Tools that have changed between versions cannot be launched when using compatible, but not corresponding, client-server combinations.
Support for paired-end reads in the Ion Torrent importer will be retired and will not be available in the the next major release of the software.
The following tools will be removed in a future release of the software:
If you are concerned about these proposed changes, please contact our Support team by emailing ts-bioinformatics@qiagen.com.
CLC Command Line Tools 6.0.3 is the corresponding client for QIAGEN CLC Genomics Server 11.0.3.
CLC Command Line Tools 6.0.3 can also act as a client for the QIAGEN CLC Genomics Server 11.0, 11.0.1, and 11.0.2. However, we recommend running the corresponding version of the CLC Command Line Tools QIAGEN CLC Genomics Server.
Some tools previously only available for use with Biomedical-enabled QIAGEN CLC Genomics Servers are now available for any QIAGEN QIAGEN CLC Genomics Server 11.0 and higher, but are legacy tools and will be retired in a future release of the software. These tools are placed within the Legacy folder of QIAGEN CLC Genomics Workbench 12.x. The relevant QIAGEN CLC Server Command Line Tools commands are:
Please also refer to the Latest Improvements listing for QIAGEN CLC Genomics Server 11.0.1 below to see all the changes that have taken place since QIAGEN CLC Genomics Server 11.0.
The maximum amount of temporary disk space for the read mapping reference cache (the temporary disk space used for reference data structure files) has been increased to 16 GB. It was previously set to 8 GB.
The following are the corresponding clients for the QIAGEN CLC Genomics Server 11.0.2.
We recommend running the corresponding versions of clients for QIAGEN CLC Genomics Server. However, QIAGEN CLC Genomics Workbench 12.0 and 12.0.1, QIAGEN CLC Main Workbench 8.1 and 8.1.1, and CLC Command Line Tools 6.0 and 6.0.1 can also connect to QIAGEN CLC Genomics Server 11.0.2. Tools that have changed between versions cannot be launched when using compatible, but not corresponding, client-server combinations.
The following functionalities of NGS importers will be retired and will not be available in the the next major release of the software:
The following tools will be removed in a future release of the software:
If you are concerned about these proposed changes, please contact our Support team by emailing ts-bioinformatics@qiagen.com.
This is a compatibility release to supply the corresponding client for QIAGEN CLC Genomics Server 11.0.2.
Some tools previously only available for use with Biomedical-enabled QIAGEN CLC Genomics Servers are now available for any QIAGEN CLC Genomics Server 11.0 and higher, but are legacy tools and will be retired in a future release of the software. These tools are placed within the Legacy folder of QIAGEN CLC Genomics Workbench 12.x. The relevant CLC Server Command Line Tools commands are:
CLC Command Line Tools 6.0.2 is the corresponding client for QIAGEN CLC Genomics Server 11.0.2.
CLC Command Line Tools 6.0.2 can also act as a client for the QIAGEN CLC Genomics Server 11.0 and 11.0.1. However, we recommend running the corresponding version of the CLC Command Line Tools QIAGEN CLC Genomics Server.
The following are the corresponding clients for the QIAGEN CLC Genomics Server 11.0.1.
We recommend running the corresponding versions of clients for QIAGEN CLC Genomics Server. However, QIAGEN CLC Genomics Workbench 12.0, QIAGEN CLC Main Workbench 8.1, and CLC Command Line Tools 6.0 can also connect to QIAGEN CLC Genomics Server 11.0.1. Tools that have changed between versions cannot be launched when using compatible, but not corresponding, client-server combinations.
The following functionalities of NGS importers will be retired and will not be available in the the next major release of the software:
The following tools will be removed in a future release of the software:
If you are concerned about these proposed changes, please contact our Support team by emailing ts-bioinformatics@qiagen.com.
CLC Command Line Tools 6.0.1 is the corresponding client for QIAGEN CLC Genomics Server 11.0.1.
CLC Command Line Tools 6.0.1 can also act as a client for the QIAGEN CLC Genomics Server 11.0. However, we recommend running the corresponding version of the CLC Command Line Tools and QIAGEN CLC Genomics Server.
A flag in the CLCGenomicsServer.vmoptions file must be removed when upgrading in place to the QIAGEN CLC Genomics Server 11.0 on macOS. Please delete “-d64” from the CLCGenomicsServer.vmoptions file, which can be found in the QIAGEN CLC Genomics Server installation area and then restart the QIAGEN CLC Genomics Server service. The -d64 option is not supported by recent versions of java. Its inclusion in the vmoptions file on macOS systems will stop the QIAGEN CLC Genomics Server from starting up.
The following tools will be removed in a future release of the software:
If you are concerned about these proposed changes, please contact our Support team by emailing ts-bioinformatics@qiagen.com.
The following are the corresponding clients for the QIAGEN CLC Genomics Server 11.0
Please see the QIAGEN CLC Genomics Server 12.0 listing for the details about the new tools and features listed below.
These tools were formerly available via the Bisulfite Sequencing Server Plugin, but are now integrated into the server software.
Command removed: ngs_import_solid
Commands changed:
contig_read_mapping Removed options: –color-error-cost, –color-space
denovo_assembly Removed options: –long-reads-color-error-cost, –long-reads-color-space
read_mapping Removed options: –color-error-cost, –color-space
rna_seq Removed options: –color-error-cost, –color-space
small_rna_annotate Removed options: –color-space
small_rna_sampling Removed options: –color-space
trim Removed options: –color-space
Some tools previously only available for use with Biomedical-enabled QIAGEN CLC Genomics Servers are now available for any QIAGEN CLC Genomics Server 12.0, but are legacy tools and will be retired in a future release of the software. These tools are placed within the Legacy folder of QIAGEN CLC Genomics Workbench 12.0. The relevant CLC Server Command Line Tools commands are:
The following are the corresponding clients for the QIAGEN CLC Genomics Server 10.0.2.
We recommend running the corresponding versions of clients for QIAGEN CLC Genomics Server. However, QIAGEN CLC Genomics Workbench 11.0 and 11.0.1, Biomedical Genomics Workbench 5.0 and 5.0.1, and CLC Command Line Tools 5.0 and 5.0.1 can also connect to QIAGEN CLC Genomics Server 10.0.2. Tools that have changed between versions cannot be launched when using compatible, but not corresponding, client-server combinations.
If you are concerned about these changes, please contact the QIAGEN Bioinformatics team (ts-bioinformatics@qiagen.com).
This is a compatibility release to supply the corresponding client for QIAGEN CLC Genomics Server 10.0.2.
CLC Command Line Tools 5.0.2 is the corresponding client for QIAGEN CLC Genomics Server 10.0.2.
CLC Command Line Tools 5.0.2 can also act as a client for the QIAGEN CLC Genomics Server 10.0 and 10.0.1. However, we recommend running the corresponding version of the CLC Command Line Tools QIAGEN CLC Genomics Server.
– When doing c. annotations (DNA-level HGVS) we annotate insertions that really are duplications as such.
– For c. annotations we furthermore fulfill the 3′ rule for insertions, deletions and duplications.
– When determining amino acid changes, the 3′ rule is applied to the DNA change first. This may shift a variant in or out of the coding region, and that will affect whether or not we consider it as an amino acid change.
The 3′ rule for p. annotations were previously fulfilled and are not affected by this fix.
The following are the corresponding clients for the QIAGEN CLC Genomics Server 10.0.1
We recommend running the corresponding versions of clients for QIAGEN CLC Genomics Server. However, QIAGEN CLC Genomics Workbench 11.0, Biomedical Genomics Workbench 5.0, and CLC Command Line Tools 5.0 can also connect to QIAGEN CLC Genomics Server 10.0.1. Tools that have changed between versions cannot be launched when using compatible, but not corresponding, client-server combinations.
If you are concerned about these changes, please contact our Support team (AdvancedGenomicsSupport@qiagen.com).
This is a compatibility release to supply the corresponding client for QIAGEN CLC Genomics Server 10.0.1.
CLC Command Line Tools 5.0.1 is the corresponding client for QIAGEN CLC Genomics Server 10.0.1
CLC Command Line Tools 5.0.1 can also act as a client for the QIAGEN CLC Genomics Server 10.0. However, we recommend running the corresponding version of the CLC Command Line Tools QIAGEN CLC Genomics Server.
If you are concerned about these changes, please contact our Support team (AdvancedGenomicsSupport@qiagen.com).
The follow software are the corresponding clients for the QIAGEN CLC Genomics Server 10.0
If you are concerned about the proposed changes, please contact our Support team (AdvancedGenomicsSupport@qiagen.com).
export-e fastq
mutation_tester_tool
small_rna_sampling
trim
export
The following are the corresponding clients for the QIAGEN CLC Genomics Server 9.1.3:
We recommend running the corresponding versions of clients for QIAGEN CLC Genomics Server. However, QIAGEN CLC Genomics Workbench 10.0.0, 10.0.1 10.1, 10.1.1 and 10.1.2, Biomedical Genomics Workbench 4.0, 4.1, 4.1.1 and 4.1.2, and CLC Command Line Tools 4.0, 4.1, 4.1.1 and 4.1.2 can also connect to QIAGEN CLC Genomics Server 9.1.3. Tools that have changed between versions cannot be launched when using compatible, but not corresponding, client-server combinations.
SOLiD colorspace data support, including import, will not be available from QIAGEN CLC Genomics Server 11.0 onwards.
This is a compatibility release to supply the corresponding client for QIAGEN CLC Genomics Server 9.1.3.
CLC Command Line Tools 4.1.3 is the corresponding client for QIAGEN CLC Genomics Server 9.1.3.
CLC Command Line Tools 4.1.3 can also act as a client for the QIAGEN CLC Genomics Server 9.1.2, 9.1.1, 9.1 and 9.0. However, we recommend running the corresponding version of the CLC Command Line Tools QIAGEN CLC Genomics Server.
The following are the corresponding clients for the QIAGEN CLC Genomics Server 9.1.2
We recommend running the corresponding versions of clients for QIAGEN CLC Genomics Server. However, QIAGEN CLC Genomics Workbench 10.0.0, 10.0.1 10.1, and 10.1.1, Biomedical Genomics Workbench 4.0, 4.1 and 4.1.1, and CLC Command Line Tools 4.0, 4.1 and 4.1.1 can also connect to QIAGEN CLC Genomics Server 9.1.2. Tools that have changed between versions cannot be launched when using compatible, but not corresponding, client-server combinations.
Support for SOLiD colorspace data will be phased out over the next 12 months. If you are concerned about the proposed change, please contact our Support team (AdvancedGenomicsSupport@qiagen.com).
This is a compatibility release to supply the corresponding client for QIAGEN CLC Genomics Server 9.1.2.
CLC Command Line Tools 4.1.2 is the corresponding client for QIAGEN CLC Genomics Server 9.1.2.
CLC Command Line Tools 4.1.2 can also act as a client for the QIAGEN CLC Genomics Server 9.1.1, 9.1 and 9.0. However, we recommend running the corresponding version of the CLC Command Line Tools QIAGEN CLC Genomics Server.
The following are the corresponding clients for the QIAGEN CLC Genomics Server 9.1.1
We recommend running the corresponding versions of clients for QIAGEN CLC Genomics Server. However, QIAGEN CLC Genomics Workbench 10.0.0, 10.0.1 and 10.1, Biomedical Genomics Workbench 4.0 and 4.1, and QIAGEN CLC Command Line Tools 4.0 and 4.1 can connect to QIAGEN CLC Genomics Server 9.1.1. Tools that have changed between versions cannot be launched when using compatible, but not corresponding, client-server combinations.
This is a compatibility release to supply the corresponding client for QIAGEN CLC Genomics Server 9.1.1.
CLC Command Line Tools 4.1.1 is the corresponding client for QIAGEN CLC Genomics Server 9.1.1.
CLC Command Line Tools 4.1.1 can also act as a client for the QIAGEN CLC Genomics Server 9.1 and 9.0. However, we recommend running the corresponding version of the CLC Command Line Tools QIAGEN CLC Genomics Server.
The following are the corresponding clients for the QIAGEN CLC Genomics Server 9.1.0
We recommend running the corresponding versions of clients for QIAGEN CLC Genomics Server. However, QIAGEN CLC Genomics Workbench 10.0.0 and 10.0.1, Biomedical Genomics Workbench 4.0, and CLC Command Line Tools 4.0 can connect to QIAGEN CLC Genomics Server 9.1.0. Tools that have changed between versions cannot be launched when using compatible, but not corresponding, client-server combinations.
This is a compatibility release to supply the corresponding client for QIAGEN CLC Genomics Server 9.1.0
CLC Command Line Tools 4.1.0 is the corresponding client for QIAGEN CLC Genomics Server 9.1.0.
CLC Command Line Tools 4.1.0 can also act as a client for the QIAGEN CLC Genomics Server 9.0. However, we recommend running the corresponding version of the CLC Command Line Tools QIAGEN CLC Genomics Server.
*Tools marked with an asterisk were available to earlier Workbench versions via the Advanced RNA-Seq plugin.
These tools automatically account for differences due to sequencing depth, removing the need to normalize input data. They work with existing RNA-seq TE and GE tracks. Changes made in this release mean that outputs from the Differential Expression for RNA-Seq tool can now be used as inputs to the Extract Annotations (for QIAGEN CLC Genomics Server) and Extract Reads Based on Overlap tools.
The follow software are the corresponding clients for the QIAGEN CLC Genomics Server 9.0
rna_seq
exporting to bam format (-A export -e bam)
rna_seq
The tool now runs with EM enabled by default.
sequencing_qc_report
The tool now generates these outputs as part of the report by default.
qc_for_sequencing_reads
We recommend running the corresponding versions of clients for QIAGEN QIAGEN CLC Genomics Server. However, QIAGEN QIAGEN CLC Genomics Workbench 9.5.4, 9.5.3, 9.5.2, 9.5.1, 9.5, 9.0.1 and 9.0, Biomedical Genomics Workbench 3.5.4, 3.5.3, 3,5.2, 3.5.1, 3.5, 3.0.1 and 3.0, and CLC Command Line Tools 3.5.4, 3.5.3, 3.5.2, 3.5.1, 3.5, 3.0.1 and 3.0 can connect to QIAGEN CLC Genomics Server 8.5.5. In addition, QIAGEN QIAGEN CLC Genomics Workbench 9.5.x and Biomedical Genomics Workbench 3.5.x and CLC Command Line Tools 3.5.x can connect to a QIAGEN QIAGEN CLC Genomics Server 8.0.x. Tools that have changed between versions cannot be launched when using compatible, but not corresponding, client-server combinations.
This is a compatibility release to supply the corresponding client for QIAGEN QIAGEN CLC Genomics Server 8.5.5.
CLC Command Line Tools 3.5.5 is the corresponding client for QIAGEN QIAGEN CLC Genomics Server 8.5.5.
CLC Command Line Tools 3.5.5 can also act as a client for the QIAGEN QIAGEN CLC Genomics Server 8.5.4, 8.5.3, 8.5.2, 8.5.1, 8.5., 8.0.1 and 8.0. However, we recommend running the corresponding version of the CLC Command Line Tools QIAGEN QIAGEN CLC Genomics Server.
We recommend running the corresponding versions of clients for QIAGEN CLC Genomics Server. However, QIAGEN CLC Genomics Workbench 9.5.3, 9.5.2, 9.5.1, 9.5, 9.0.1 and 9.0, Biomedical Genomics Workbench 3.5.3, 3,5.2, 3.5.1, 3.5, 3.0.1 and 3.0, and CLC Command Line Tools 3.5.3, 3.5.2, 3.5.1, 3.5, 3.0.1 and 3.0 can connect to QIAGEN CLC Genomics Server 8.5.4. In addition, QIAGEN CLC Genomics Workbench 9.5.x and Biomedical Genomics Workbench 3.5.x and CLC Command Line Tools 3.5.x can connect to a QIAGEN CLC Genomics Server 8.0.x. Tools that have changed between versions cannot be launched when using compatible, but not corresponding, client-server combinations.
This is a compatibility release to supply the corresponding client for QIAGEN CLC Genomics Server 8.5.4.
CLC Command Line Tools 3.5.4 is the corresponding client for QIAGEN CLC Genomics Server 8.5.4.
CLC Command Line Tools 3.5.4 can also act as a client for the QIAGEN CLC Genomics Server 8.5.3, 8.5.2, 8.5.1, 8.5., 8.0.1 and 8.0. However, we recommend running the corresponding version of the CLC Command Line Tools QIAGEN CLC Genomics Server.
For the Basic Variant Detection, Fixed Ploidy Variant Detection and Low Frequency Variant Detection tools, the following have been addressed:
The above issues, including information on the products affected, are described on the public notification page: Coverage and count reporting for variants in certain circumstances are incorrect
For the Identify Known Mutations from Sample Mappings tool, the following issues have been addressed:
We recommend running the corresponding versions of clients for QIAGEN CLC Genomics Server. However, QIAGEN CLC Genomics Workbench 9.5.2, 9.5.1, 9.5, 9.0.1 and 9.0, Biomedical Genomics Workbench 3,5.2, 3.5.1, 3.5, 3.0.1 and 3.0, and CLC Command Line Tools 3.5.2, 3.5.1, 3.5, 3.0.1 and 3.0 can connect to QIAGEN CLC Genomics Server 8.5.3. In addition, QIAGEN CLC Genomics Workbench 9.5.x and Biomedical Genomics Workbench 3.5.x and CLC Command Line Tools 3.5.x can connect to a QIAGEN CLC Genomics Server 8.0.x. Tools that have changed between versions cannot be launched when using compatible, but not corresponding, client-server combinations.
This is a compatibility release to supply the corresponding client for QIAGEN CLC Genomics Server 8.5.3.
CLC Command Line Tools 3.5.3 is the corresponding client for QIAGEN CLC Genomics Server 8.5.3.
CLC Command Line Tools 3.5.3 can also act as a client for the QIAGEN CLC Genomics Server 8.5.2, 8.5.1, 8.5., 8.0.1 and 8.0. However, we recommend running the corresponding version of the CLC Command Line Tools QIAGEN CLC Genomics Server.
We recommend running the corresponding versions of clients for QIAGEN CLC Genomics Server. However, QIAGEN CLC Genomics Workbench 9.5.1, 9.5, 9.0.1 and 9.0, Biomedical Genomics Workbench 3.5.1, 3.5, 3.0.1 and 3.0, and CLC Command Line Tools 3.5.1, 3.5, 3.0.1 and 3.0 can connect to QIAGEN CLC Genomics Server 8.5.2. In addition, QIAGEN CLC Genomics Workbench 9.5.x and Biomedical Genomics Workbench 3.5.x and CLC Command Line Tools 3.5.x can connect to a QIAGEN CLC Genomics Server 8.0.x. Tools that have changed between versions cannot be launched when using compatible, but not corresponding, client-server combinations.
This is a compatibility release to supply the corresponding client for QIAGEN CLC Genomics Server 8.5.2.
CLC Command Line Tools 3.5.2 is the corresponding client for QIAGEN CLC Genomics Server 8.5.2.
CLC Command Line Tools 3.5.2 can also act as a client for the QIAGEN CLC Genomics Server 8.5.1, 8.5., 8.0.1 and 8.0. However, we recommend running the corresponding version of the CLC Command Line Tools QIAGEN CLC Genomics Server.
We recommend running the corresponding versions of clients for QIAGEN CLC Genomics Server. However, QIAGEN CLC Genomics Workbench 9.5, 9.0 and 9.0.1, Biomedical Genomics Workbench 3.5, 3.0 and 3.0.1, and CLC Command Line Tools 3.5, 3.0 and 3.0.1 can connect to QIAGEN CLC Genomics Server 8.5.1. In addition, QIAGEN CLC Genomics Workbench 9.5.1, Biomedical Genomics Workbench 3.5.1 and CLC Command Line Tools 3.5.1 can connect to a QIAGEN CLC Genomics Server 8.0.x. Tools that have changed between versions cannot be launched when using compatible, but not corresponding, client-server combinations.
This is a compatibility release to supply the corresponding client for the QIAGEN CLC Genomics Server x.x.x.
CLC Command Line Tools 3.5.1 is the corresponding client for QIAGEN CLC Genomics Server 8.5.1.
CLC Command Line Tools 3.5.1 can act as a client for the QIAGEN CLC Genomics Server 8.5, 8.0 and 8.0.1. However, we recommend running the corresponding version of the CLC Command Line Tools QIAGEN CLC Genomics Server.
We recommend running the corresponding versions of clients for the QIAGEN CLC Genomics Server. However, QIAGEN CLC Genomics Workbench 9.0 and 9.0.1, Biomedical Genomics Workbench 3.0 and 3.0.1, and CLC Command Line Tools 3.0 and 3.0.1 can connect to the QIAGEN CLC Genomics Server 8.5. In addition, the QIAGEN CLC Genomics Workbench 9.5, Biomedical Genomics Workbench 3.5 and CLC Command Line Tools 3.5 can can connect to a QIAGEN CLC Genomics Server 8.0.x. Tools that have changed between versions cannot be launched when using compatible, but not corresponding, client-server combinations.
From now on, only 64 bit versions of the QIAGEN CLC Genomics Server, QIAGEN CLC Genomics Workbench, Biomedical Genomics Workbench, CLC Bioinformatics Database and QIAGEN CLC Assembly Cell will be made available. 32 bit versions of these are discontinued.
CLC Command Line Tools 3.5 is the corresponding client for QIAGEN CLC Genomics Server 8.5.
CLC Command Line Tools 3.5 can act as a client for the QIAGEN CLC Genomics Server 8.0 and 8.0.1. However, we recommend running the corresponding version of the CLC Command Line Tools QIAGEN CLC Genomics Server.
From now on, only 64 bit versions of the QIAGEN CLC Genomics Server, QIAGEN CLC Genomics Workbench, Biomedical Genomics Workbench, CLC Bioinformatics Database and QIAGEN CLC Assembly Cell will be made available. 32 bit versions of these are discontinued.
CLC Command Line Tools 3.0.1 is the corresponding client for QIAGEN CLC Genomics Server 8.0.1.
CLC Command Line Tools 3.0.1 and 3.0 can act as clients for the QIAGEN CLC Genomics Server 8.0.1. However, we generally recommend running the corresponding version of the CLC Command Line Tools QIAGEN CLC Genomics Server.
From the autumn 2016 release, only 64 bit versions of the QIAGEN CLC Genomics Server, QIAGEN CLC Genomics Workbench, Biomedical Genomics Workbench, CLC Bioinformatics Database and QIAGEN CLC Assembly Cell will be made available. 32 bit versions of these will be discontinued from that time.
These replacements apply to Biomedical Genomics Server Extension users only
All changes in this release have also been fixed on the QIAGEN QIAGEN CLC Genomics Server 9.x and 8.5.x lines at time of writing.
We recommend running the corresponding versions of clients for QIAGEN CLC Genomics Server. The following are the corresponding client software for the QIAGEN CLC Genomics Server 7.5.4:
The following client software and versions are compatible with the QIAGEN CLC Genomics Server 7.5.4:
Compatible client versions that are not the corresponding version can connect to QIAGEN CLC Genomics Server 7.5.4. Jobs can be launched on the server from such client software with the exception of jobs where the tool being run has changed between between the client software version and the server software version.
This version of the CLC Server Command Line Tools is the corresponding client version for the QIAGEN CLC Genomics Server 7.5.3.
This version of the CLC Server Command Line Tools can be used to connect to the QIAGEN CLC Genomics Server 7.5.3, 7.5.2, 7.5.1, 7.5, 7.0.3, 7.0.2, 7.0.1 and 7.0. However, we generally recommend running the corresponding client for the server version.
On Windows some temporary files named MIMEXXX.tmpwas not removed on exit
This version of the CLC Server Command Line Tools is the corresponding client version for the QIAGEN CLC Genomics Server 7.5.2.
This version of the CLC Server Command Line Tools can be used to connect to the QIAGEN CLC Genomics Server 7.5.2, 7.5.1, 7.5, 7.0.3, 7.0.2, 7.0.1 and 7.0. However, we generally recommend running the corresponding client for the version of the QIAGEN CLC Genomics Server being connected to.
Tools that have changed parameters
This release contains fixes to issues seen sporadically on CLC Servers with job nodes, where the main symptom is the occasional occurrence of irreproducible errors related to locating data when you run a job. If you are running a single server, or a master server with grid nodes, or if your job node setup is running without problems, then you do not need to upgrade to this version.
The QIAGEN CLC Genomics Server 6.5.2 is compatible with the QIAGEN CLC Genomics Workbench 6.5.1 and the CLC Command Line Tools 2.2.1.
The QIAGEN CLC Genomics Server 6.5.2 with Cancer Research Add-on is compatible with the CLC Cancer Research Workbench 1.5.2 and the CLC Command Line Tools 2.2.1.
An option to change the way workflows are submitted to the grid has been introduced. The behaviour of the previous version (and if the property is unset or set to false) is to submit each individual job in the workflow when its dependencies have been executed. The consequence of this is that jobs from different workflows are interleaved in execution. If many workflows are executed at the same time, this means that total run time of a workflow becomes very unpredictable.
By creating a properties file in the server installation directory: /settings/grid.properties
containing one line: “com.clcbio.server.configuration.grid.lsfPreserveWorkflowOrder = true
, and restarting the server, a new behavior can be switched on. With this new behavior all jobs of the workflow are submitted at once, supplying the grid with the dependency information. The consequence of this is that all jobs belonging to one workflow are placed next to each other in the execution queue on the grid. The general execution order of the jobs is therefore, that the workflow submitted first will be completed before jobs from the next workflow is run. It should be noted that if the grid has sufficient resources and all elements of the first workflow are waiting for the execution of an element, elements from the next workflow will be executed.
For this release, this behavior is only supported for LSF grids.
One drawback of submitting the entire workflow at once is that a large number of grid jobs are created (#elements-per-workflow x #workflows). The server creates a new thread for each job on the grid, which it uses to poll for status with 5 second intervals. This does not work very well if there are many grid jobs. By adding a line: com.clcbio.server.configuration.grid.groupedPolling = true
in the /settings/grid.properties
file and restarting the server, this is changed such that a single thread is used to poll the status of all grid jobs. This reduces both the number of threads used but also allows for more efficient polling techniques against the DRMAA library.
The behavior described above is expected to be the default behavior with next major release of the QIAGEN CLC Genomics Server (check latest improvements notes for confirmation).
Adding support for CLC Cancer Research Workbench: If you have purchased a QIAGEN CLC Genomics Server with added support for Cancer Research, you will receive an additional license that will allow Cancer Research-specific tools to be executed on the QIAGEN CLC Genomics Server.
This release of the QIAGEN CLC Genomics Server 5.0 is compatible with CLC Server Command Line Tools 1.7
Important: In Genomics Workbench 5.5, the Process Tagged Sequences tool would sometimes switch the sample names of the results. We strongly recommend everybody to update to the new version, and re-run all analyses made with this tool in Genomics Workbench 5.5.
This release of the QIAGEN CLC Genomics Server 4.5 is compatible with CLC Server Command Line Tools 1.6
Ion Torrent paired protocols are now supported for both fastq and sff files.
See a list of all plug-ins here. The pdf documentation of all plug-ins has been updated as well.
RNA-Seq would crash when selecting prokaryote as organism type
Please note that you need to upgrade the Workbench plug-in in order to connect to the new server and you will also need to update the Command Line Tools client
This update is recommended for all users.